5.2 Main Analysis
- Alpha Diversity Plot - A.
* Beta Diversity Plot - A.
* Beta Diversity Plot - B.
* Permutational analysis of variance
- Relative abundance of the top 50 ASVs
NBIS ID: SMS_6198
Report Version: 1.0
Request by: Mona N. Högberg (mona.n.hogberg@slu.se)
Principal Investigator: Mona N. Högberg (mona.n.hogberg@slu.se)
Organisation: SLU
NBIS Staff: Juliana Assis (juliana.assis@nbis.se)
## LIBRARIES
library("dada2")
library("devtools")
library("dplyr")
library("ggplot2")
library("microbiome")
library("phangorn")
library("phyloseq")
library("Rcpp")
library("reshape2")
library("tidyr")
library("vegan")
library("ShortRead")
library("Biostrings")
library("DECIPHER")
library("SensusR")
library("gplots")
library("gridExtra")
library("grid")
library("ggpubr")
library("reshape2")
library("reshape")
library("lulu")
library("ggrepel")
library("ggh4x")
library("RColorBrewer")
library("rITSx")
library("MicEco")1.0
96 samples
ITS amplicon
Data location rackham.uppmax.uu.se /proj/snic2022-22-352
Uppmax project ID SNIC 2022/22-352
NGI Project ID P9723
Database used Unite
NFCore-Ampliseq (Dada2)
#Sample Info
head(sample_info_tab)Alpha Diversity Plot comparing the Replicates A and B.
Quality control analysis using matched samples from 3 different Transects: A, B and C of the experiment and replicates samples on each Ecotype. Comparison of alpha diversity in technical replicates samples on all Ecotypes from each Transect. ASV richness and ASV Shannon diversity.
* Beta Diversity Plot comparing the Replicates A and B.
Rarefaction
* Beta Diversity Plot - A.
* Beta Diversity Plot - B.
* Permutational analysis of variance
Help is needed with running the “nfcore/ampliseq” pipeline developed at NGI for the analyses of fungal ITS1 amplicons, Illumina Miseq analysis NGI project ID P5953 (M.Hogberg_17_01_project summary from 2018-01-19 by Chuan Wang refers to P9723, >=Q30 (mean(SD), 70(2) (%), Sum Reads=15 650 000, Mean reads per sample 171 711, 1 pool of amplicons, 1 flowcell v3, PE 2x301bp (validated method), demultiplexing, quality control and raw data delivery on Uppmax (validated method). Agreement number M.Hogberg_16_01-20160826. Grus delivery project delivery 00654. Because my support application 2019-01-17 was rejected, I have collaborated with partners in US on this matter but all is extremely delayed for known reasons. I got some hope today when I read about the recently developed pipeline for fungal analyses! Unfortunately, I have no programming skills but have a BSc in Molecular Biology.
Short summary of the work.
Further steps to be taken (if needed).
Relevant references for methods, tools etc.
Files delivered to the user with descriptions.
/data/processed/b/
8 directories, 18 filesTotal size is XX GB.
The responsibility for data archiving lies with the PI of the project. We do not offer long-term storage or retrieval of data.
If you are presenting the results in a paper, at a workshop or conference, we kindly ask you to acknowledge us.
“Support by NBIS (National Bioinformatics Infrastructure Sweden) is gratefully acknowledged.”
“The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project SNIC 2022-22-352.”
“The authors would like to acknowledge support from Science for Life Laboratory (SciLifeLab), the National Genomics Infrastructure (NGI), and Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) for providing assistance in massive parallel sequencing and computational infrastructure.”
You should soon be contacted by one of our managers with a request to close down the project in our internal system and for invoicing matters. If we do not hear from you within 30 days the project will be automatically closed and invoice sent. Again, we would like to remind you about data responsibility and acknowledgements, see sections: Data Responsibility and Acknowledgments.
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